5C0W

Structure of a 12-subunit nuclear exosome complex bound to single-stranded RNA substrates

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

RNA degradation paths in a 12-subunit nuclear exosome complex.

Makino, D.L., Schuch, B., Stegmann, E., Baumgartner, M., Basquin, C., Conti, E.

(2015) Nature 524: 54-58

  • DOI: 10.1038/nature14865
  • Primary Citation of Related Structures:  
    5C0W, 5C0X, 5C0Y

  • PubMed Abstract: 

    • The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs ...

    The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs. The combined structural and biochemical data of this 12-subunit complex reveal how a single-stranded RNA can reach the Rrp44 or Rrp6 active sites directly or can bind Rrp6 and be threaded via the central channel towards the distal RNase Rrp44. When a bulky RNA is stalled at the entrance of the channel, Rrp6-Rrp47 swings open. The results suggest how the same molecular machine can coordinate processive degradation and partial trimming in an RNA-dependent manner by a concerted swinging mechanism of the two RNase subunits.

    Organizational Affiliation: 

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45A305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45, YDR280W, D9954.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6B248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6, ECM20, RRP41, YGR195W, G7587
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43C394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43, YCR035C, YCR35C, YCR522
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46D245Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46, YGR095C
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42E267Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RRP42, YDL111C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3F250Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: MTR3, YGR158C, G6676
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40G243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40, YOL142W
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4H361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4, YHR069C
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4I295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4, SKI4, YNL232W, N1154
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3J1,004Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: DIS3, RRP44, YOL021C, O2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease RRP6K695Saccharomyces cerevisiae S288CMutation(s): 2 
Gene Names: RRP6, UNC733, YOR001W
EC: 3.1.13
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex protein LRP1L184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1, RRP47, YC1D, YHR081W
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Entity ID: 13
MoleculeChainsLengthOrganismImage
RNA syntheticN,
M [auth R]		18synthetic construct
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
P [auth J]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
O [auth J]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.277 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.38α = 90
b = 195.38β = 90
c = 463.65γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European CommissionGermanyERC 294371
European CommissionGermanyMarie Curie ITN RNPnet
German Research FoundationGermanySFB646, SFB1035, GRK1721, FOR1680, CIPSM
Louis JeantetGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations